Some of the problems
in evolutionary theory concern the speed of speciation. It
is clear from the geological record that this has not always
been smooth. One of the reasons why Cuvier disagreed with
Lamarck in the early nineteenth century is that he was able
to discredit Lamarck’s idea of the transformation of species
by pointing to the fact that the fossil evidence, as it was
known then, was also consistent with multiple periods of
creation. The record was that patchy, and it was also clear
that some species remained essentially unchanged for very
long periods of time (stasis). In the twentieth century,
with much more evidence to consider, Eldredge and Gould in
1971 proposed the theory of punctuated equilibrium to
account for the fact that most fossil species show long
periods of stasis, and that rapid (on a geological time
scale) changes occurred more rarely and were important
periods of speciation. The difference between their theory
and that of Cuvier was that Eldredge and Gould were simply
proposing that evolutionary change from a common ancestor
does not happen at a constant speed, whereas Cuvier
interpreted the evidence to show that there had been
multiple creations.

Darwin also realised
that evolutionary change could not always have been smooth.
In the fourth edition of
The Origin of Species
he wrote “the periods during which species have undergone
modification, though long as measured in years, have
probably been short in comparison with the periods during
which they retain the same form.” This is, in essence,
Eldredge and Gould’s idea of punctuated equilibrium.

There has been much
argument about what precisely is meant by ‘punctuated’. A
gradual change over a hundred thousand or a million or even
a few million years will appear rapid on a geological time
scale of hundreds of millions of years. The Cambrian
explosion that occurred over 500 million years ago is a good
example. Within just 20 million years all the phyla in
existence today had developed. The standard response to
these kinds of theories has therefore been that they are
entirely consistent with neo-darwinism. Changes in selection
pressure due to environmental changes or geographic
distribution, and the occasional catastrophic environmental
change, might account for the observed variations in speed
of change without supposing additional mechanisms of change.

The new evidence from
work on symbiogenesis, the various forms of inheritance of
acquired characteristics, genetic assimilation, natural
genetic engineering, including genome change and
reorganisation over and above the accumulation of chance
mutations, changes the situation in more fundamental ways
that require either extensions of or replacement of the
modern synthesis. These mechanisms resemble punctuated
equilibrium theories in proposing that evolution can occur
in jumps. Since these can be very sudden indeed it is best
to use a word different from ‘punctuated’ to avoid confusion
with Eldredge and Gould’s theory. ‘Saltatory’ means jumping.
The new mechanisms produce saltations of various kinds:

Symbiogenesis
is the fusion of two species. The best established example
of this is the bacterial origin of mitochondria and
chloroplasts and, perhaps, other organelles. Clearly, this
process is the ultimate in ‘saltation’. It depends on
processes of cellular ingestion that are natural in the
feeding activity of unicellular organisms and, on an
evolutionary timescale, it is therefore very rapid indeed.
Of course, subsequent changes can then also occur more
slowly. We know, for example, that some of the ingested DNA
in what became organelles eventually moved to the nucleus in
eukaryotes.

Endosymbiosis: Homage to Lynn Margulis, a painting by
Shoshanah Dubineer, occupies a hallway in the Morrill
Science Center at the University of Massachusetts, Amherst,
where Margulis was a professor until her death in 2011.
Margulis maintained that genetic variation emerges primarily
through symbiosis, not through competition.

Natural genetic engineering could also
occur within a single generation. Reorganisations of genomes
involving duplications, deletions and insertions of long
sequences, would be essentially instantaneous on a
geological timescale. Defenders of the modern synthesis have
argued that speciation due to such changes, and
symbiogenesis, should not be classified as punctuated
equilibrium. That is correct in the sense that it was not
what Eldridge and Gould had in mind. But so far as timescale
is concerned such changes would be saltatory in the ordinary
sense of the word. They would be even more sudden than the
punctuations proposed by Eldredge and Gould.

Genetic assimilation can also occur
rapidly. Waddington’s mid-twentieth century experiments
showed that an induced acquired characteristic in fruit
flies could become permanent (assimilated) within fourteen
generations. This must have represented the time required
for selection for an induced characteristic to bring
together in a single genome all the relevant alleles for
that characteristic to be passed on to subsequent
generations without the inducing environmental stimulus.
Waddington coined the term ‘epigenetics’ to describe his
discovery. Today, epigenetics usually refers to genome and
chromatin marking.

Inheritance of acquired characteristics through the
persistence of epigenetic effects through successive
generations can also speed up the evolutionary process.
These transgenerational environmental influences should
spread through a population much more rapidly since it is
possible for a large fraction of the population to be
subject to the same changes at the same time. There is no
need to wait for a single DNA change to spread slowly
through a population. The orthodox response to this
mechanism is to dismiss it as transient, which it certainly
is in some cases. But there are now examples of such
transmission over many generations and which show the same
degree of strength as standard genetic transmission. Since
such effects would not need to occur very frequently, the
difficulty in identifying them experimentally would be
perfectly understandable. Speciation itself is a rare event.

While there can be
considerable uncertainty about the relative contributions of
the different mechanisms to evolutionary change, two
conclusions seem clear. The first is that, with a variety of
mechanisms open to the evolutionary process, the speed of
evolution should be faster. The second is that it is
probable that the relative contributions varied at different
stages in evolution.